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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.34.dev0

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        MultiQC is developed by Seqera.

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        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2026-02-06, 08:44 EST based on data in: /Users/kwi2002/Downloads/20260114_FastQC_MultiQC
        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 1502 samples.

        Created with MultiQC

        Mosdepth

        Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.https://github.com/brentp/mosdepthDOI: 10.1093/bioinformatics/btx699

        Cumulative coverage distribution

        Proportion of bases in the reference genome with, at least, a given depth of coverage. Calculated across the entire genome length

        For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

        Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

        For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

        Created with MultiQC

        Average coverage per contig

        Average coverage per contig or chromosome

        Created with MultiQC

        XY coverage

        Created with MultiQC

        Picard

        Tools for manipulating high-throughput sequencing data.http://broadinstitute.github.io/picard

        Variant Calling Metrics

        Showing 469/469 rows and 7/27 columns.
        Sample NameHet/Hom Ratio%GQ0Total GQ0Total Het DepthTotal SNPsdbSNP SNP countNovel SNPsFiltered SNPsFraction in dbSNP (SNPs)Ti/Tv ratio (dbSNP)Ti/Tv ratio (Novel)Indels (Total)Indels (Novel)Indels (Filtered)% in dbSNP (Indels)Indels (dbSNP)Indel Ratio (dbSNP)Indel Ratio (Novel)Multiallelic SNPs (Total)Multiallelic SNPs (dbSNP)Complex Indels (Total)Complex Indels (dbSNP)SNP Ref. BiasSingletonsTotal CalledTotal Called (known)Total Called (novel)
        S-250505-00334
        0.3
        0.0
        21051
        1589813
        1398161
        1198328
        199833
        0
        0.9
        2.1
        1.7
        165465
        26247
        0
        0.8
        139218
        0.9
        0.4
        782
        621
        86007
        74679
        0.6
        360349
        1650415
        1412846
        237569
        S-250505-00686
        0.3
        0.0
        20254
        1713579
        1672038
        1405974
        266064
        0
        0.8
        2.1
        0.9
        216843
        33042
        0
        0.8
        183801
        0.8
        0.4
        944
        761
        141376
        121821
        0.5
        495902
        2031201
        1712357
        318844
        S-250505-00689
        0.5
        0.0
        23617
        3250612
        2211448
        1659515
        551933
        0
        0.8
        2.0
        0.6
        260753
        43586
        0
        0.8
        217167
        0.8
        0.4
        1426
        1170
        176412
        151827
        0.5
        842200
        2650039
        2029679
        620360
        S-250519-00843
        0.3
        0.0
        17473
        1186521
        1384197
        1198280
        185917
        0
        0.9
        2.1
        1.3
        183145
        28805
        0
        0.8
        154340
        0.8
        0.4
        672
        552
        115098
        99737
        0.5
        342219
        1683112
        1452909
        230203
        S-250603-01359
        0.2
        0.0
        17202
        1082980
        1349445
        1139789
        209656
        0
        0.8
        2.0
        1.0
        175913
        26795
        0
        0.8
        149118
        0.8
        0.4
        602
        466
        111328
        96368
        0.5
        326996
        1637288
        1385741
        251547
        S-250603-01361
        0.3
        0.0
        17791
        1298180
        1393108
        1182411
        210697
        0
        0.8
        2.1
        1.2
        183884
        30889
        0
        0.8
        152995
        0.8
        0.4
        748
        587
        121018
        103757
        0.5
        358679
        1698758
        1439750
        259008
        S-250603-01362
        0.3
        0.0
        17453
        1375574
        1545654
        1335224
        210430
        0
        0.9
        2.1
        1.2
        196192
        32523
        0
        0.8
        163669
        0.8
        0.4
        786
        619
        120049
        101986
        0.5
        394304
        1862681
        1601498
        261183
        S-250603-01364
        0.3
        0.0
        19682
        1197014
        1434048
        1256737
        177311
        0
        0.9
        2.1
        1.3
        196634
        30215
        0
        0.8
        166419
        0.8
        0.4
        696
        593
        132299
        114039
        0.5
        379117
        1763677
        1537788
        225889
        S-250603-01367
        0.2
        0.0
        17967
        1184454
        1358094
        1155694
        202400
        0
        0.9
        2.1
        1.6
        182385
        31860
        0
        0.8
        150525
        0.8
        0.4
        696
        558
        116127
        100070
        0.5
        330030
        1657302
        1406847
        250455
        S-250603-01368
        0.3
        0.0
        19289
        1688620
        1645994
        1426633
        219361
        0
        0.9
        2.1
        1.5
        219742
        36595
        0
        0.8
        183147
        0.8
        0.4
        927
        736
        140635
        120126
        0.5
        477318
        2007298
        1730642
        276656
        S-250603-01369
        0.3
        0.0
        21687
        1294060
        1500618
        1328564
        172054
        0
        0.9
        2.1
        1.3
        203405
        31496
        0
        0.8
        171909
        0.8
        0.4
        838
        677
        134664
        115343
        0.5
        408855
        1839525
        1616493
        223032
        S-250603-01371
        0.2
        0.0
        18143
        926912
        1236846
        1074224
        162622
        0
        0.9
        2.1
        1.3
        167247
        25766
        0
        0.8
        141481
        0.8
        0.4
        535
        398
        106798
        92296
        0.5
        279277
        1511426
        1308399
        203027
        S-250603-01374
        0.3
        0.0
        19112
        1463433
        1542441
        1342723
        199718
        0
        0.9
        2.1
        1.5
        208234
        34872
        0
        0.8
        173362
        0.8
        0.4
        831
        639
        136441
        117126
        0.5
        423181
        1887947
        1633850
        254097
        S-250603-01375
        0.5
        0.0
        27705
        3250856
        2348965
        2079249
        269716
        0
        0.9
        2.1
        1.4
        311928
        50921
        0
        0.8
        261007
        0.8
        0.4
        1615
        1334
        200386
        169817
        0.5
        915440
        2862894
        2511407
        351487
        S-250603-01377
        0.3
        0.0
        17975
        1251479
        1437175
        1263430
        173745
        0
        0.9
        2.1
        1.5
        196534
        30985
        0
        0.8
        165549
        0.8
        0.4
        715
        586
        129495
        111618
        0.5
        370870
        1763919
        1541183
        222736
        S-250603-01378
        0.3
        0.0
        24084
        1670466
        1709303
        1513110
        196193
        0
        0.9
        2.1
        1.4
        228426
        36450
        0
        0.8
        191976
        0.8
        0.5
        988
        789
        147490
        125162
        0.5
        517472
        2086207
        1831037
        255170
        S-250603-01379
        0.4
        0.0
        24433
        2766420
        2185805
        1909591
        276214
        0
        0.9
        2.1
        1.5
        291533
        49586
        0
        0.8
        241947
        0.8
        0.4
        1498
        1215
        185458
        156691
        0.5
        762601
        2664294
        2309444
        354850
        S-250603-01380
        0.2
        0.0
        20492
        1099111
        1409247
        1247408
        161839
        0
        0.9
        2.1
        1.5
        194455
        29486
        0
        0.8
        164969
        0.8
        0.4
        712
        591
        134662
        116161
        0.5
        348144
        1739076
        1529129
        209947
        S-250603-01381
        0.3
        0.0
        18423
        1088922
        1372329
        1205884
        166445
        0
        0.9
        2.1
        1.6
        178007
        27580
        0
        0.8
        150427
        0.8
        0.4
        647
        525
        111222
        95564
        0.5
        336564
        1662205
        1452400
        209805
        S-250603-01383
        0.3
        0.0
        23005
        1317223
        1523073
        1363830
        159243
        0
        0.9
        2.1
        1.5
        214270
        32861
        0
        0.8
        181409
        0.8
        0.4
        850
        709
        148752
        128168
        0.5
        420516
        1886945
        1674116
        212829
        S-250603-01385
        0.3
        0.0
        20694
        2072954
        1805114
        1548660
        256454
        0
        0.9
        2.1
        1.3
        239134
        40567
        0
        0.8
        198567
        0.8
        0.4
        1045
        865
        154058
        132053
        0.5
        566874
        2199351
        1880145
        319206
        S-250603-01387
        0.3
        0.0
        21915
        1683489
        1668180
        1453234
        214946
        0
        0.9
        2.1
        1.4
        229304
        36400
        0
        0.8
        192904
        0.8
        0.4
        893
        729
        154667
        133473
        0.5
        500894
        2053044
        1780340
        272704
        S-250603-01388
        0.2
        0.0
        16582
        1002309
        1233823
        1051842
        181981
        0
        0.9
        2.1
        1.4
        159691
        27942
        0
        0.8
        131749
        0.8
        0.4
        484
        410
        94291
        80623
        0.5
        263262
        1488289
        1264624
        223665
        S-250603-01390
        0.3
        0.0
        25272
        1568018
        1644719
        1446612
        198107
        0
        0.9
        2.1
        1.2
        230447
        35929
        0
        0.8
        194518
        0.8
        0.4
        888
        737
        163425
        141159
        0.5
        495191
        2039479
        1783026
        256453
        S-250603-01393
        0.2
        0.0
        18685
        936118
        1283553
        1138309
        145244
        0
        0.9
        2.1
        1.5
        169141
        25939
        0
        0.8
        143202
        0.8
        0.4
        545
        425
        103677
        88427
        0.5
        291145
        1556916
        1370363
        186553
        S-250603-01396
        0.3
        0.0
        25899
        1130181
        1485594
        1339890
        145704
        0
        0.9
        2.1
        1.3
        212862
        31477
        0
        0.9
        181385
        0.8
        0.4
        792
        661
        151807
        130908
        0.5
        401881
        1851055
        1652844
        198211
        S-250603-01398
        0.3
        0.0
        22185
        1860996
        1739060
        1492689
        246371
        0
        0.9
        2.0
        1.1
        236508
        36981
        0
        0.8
        199527
        0.8
        0.4
        1032
        856
        157408
        136194
        0.5
        545610
        2134008
        1829266
        304742
        S-250603-01401
        0.4
        0.0
        29424
        1955733
        1866307
        1660709
        205598
        0
        0.9
        2.1
        1.1
        267200
        40625
        0
        0.8
        226575
        0.8
        0.4
        1240
        1045
        195113
        167285
        0.5
        637657
        2329860
        2055614
        274246
        S-250603-01402
        0.2
        0.0
        16927
        1063308
        1306197
        1111174
        195023
        0
        0.9
        2.1
        1.2
        172587
        28027
        0
        0.8
        144560
        0.8
        0.4
        559
        443
        109841
        94923
        0.5
        305054
        1589184
        1351100
        238084
        S-250603-01404
        0.3
        0.0
        19585
        1627423
        1625734
        1412767
        212967
        0
        0.9
        2.1
        1.4
        216898
        35726
        0
        0.8
        181172
        0.8
        0.4
        888
        698
        141196
        121450
        0.5
        473843
        1984716
        1716087
        268629
        S-250605-00261
        0.3
        0.0
        20210
        2007545
        1732630
        1409565
        323065
        0
        0.8
        2.0
        0.8
        222974
        36776
        0
        0.8
        186198
        0.8
        0.4
        997
        813
        146229
        126133
        0.5
        534421
        2102830
        1722709
        380121
        S-250605-00294
        0.3
        0.0
        25900
        1790228
        1802493
        1522426
        280067
        0
        0.8
        2.1
        0.8
        236634
        35144
        0
        0.9
        201490
        0.8
        0.4
        996
        851
        163988
        141528
        0.5
        545981
        2204111
        1866295
        337816
        S-250605-00299
        0.2
        0.0
        18187
        919753
        1237966
        1061866
        176100
        0
        0.9
        2.1
        1.3
        167205
        26622
        0
        0.8
        140583
        0.8
        0.4
        623
        485
        111728
        96324
        0.5
        286510
        1517522
        1299258
        218264
        S-250606-00019
        0.3
        0.0
        18935
        1189741
        1409384
        1168573
        240811
        0
        0.8
        2.1
        0.9
        181291
        29079
        0
        0.8
        152212
        0.8
        0.4
        636
        497
        118156
        102064
        0.5
        358237
        1709467
        1423346
        286121
        S-250606-00024
        0.3
        0.0
        19820
        1343544
        1542829
        1350518
        192311
        0
        0.9
        2.1
        1.4
        198193
        32905
        0
        0.8
        165288
        0.8
        0.4
        769
        626
        122393
        103263
        0.5
        397977
        1864184
        1619695
        244489
        S-250606-00029
        0.4
        0.0
        29598
        1679179
        1821995
        1628681
        193314
        0
        0.9
        2.1
        0.9
        248132
        34766
        0
        0.9
        213366
        0.8
        0.4
        970
        828
        171712
        147401
        0.5
        593073
        2242809
        1990276
        252533
        S-250606-00034
        0.4
        0.0
        29761
        2159661
        1975628
        1782445
        193183
        0
        0.9
        2.1
        1.3
        280807
        40839
        0
        0.9
        239968
        0.8
        0.4
        1228
        1050
        201936
        173379
        0.5
        707485
        2459599
        2196842
        262757
        S-250606-00039
        0.3
        0.0
        17911
        1506466
        1538210
        1261611
        276599
        0
        0.8
        2.0
        0.9
        195656
        31481
        0
        0.8
        164175
        0.8
        0.4
        736
        604
        125234
        107678
        0.5
        417231
        1859836
        1534068
        325768
        S-250606-00114
        0.3
        0.0
        17591
        1090690
        1358855
        1166311
        192544
        0
        0.9
        2.1
        1.3
        182214
        29057
        0
        0.8
        153157
        0.8
        0.4
        641
        505
        118588
        102348
        0.5
        334589
        1660298
        1422321
        237977
        S-250606-00438
        0.3
        0.0
        19146
        1224510
        1419920
        1257023
        162897
        0
        0.9
        2.1
        1.8
        195966
        30512
        0
        0.8
        165454
        0.8
        0.4
        708
        554
        128575
        110792
        0.5
        366322
        1745169
        1533823
        211346
        S-250606-00442
        0.4
        0.0
        23359
        2539106
        2083137
        1744323
        338814
        0
        0.8
        2.1
        0.9
        262968
        43919
        0
        0.8
        219049
        0.8
        0.4
        1196
        984
        164015
        138427
        0.5
        696392
        2511316
        2102783
        408533
        S-250609-00223
        0.4
        0.0
        35053
        2539935
        2266936
        2081981
        184955
        0
        0.9
        2.1
        1.3
        318961
        48055
        0
        0.8
        270906
        0.8
        0.5
        1692
        1496
        228429
        193189
        0.5
        872344
        2816018
        2547572
        268446
        S-250609-00510
        0.2
        0.0
        16152
        1114590
        1394736
        1206330
        188406
        0
        0.9
        2.1
        1.7
        189399
        32099
        0
        0.8
        157300
        0.8
        0.4
        737
        587
        121532
        104560
        0.5
        321490
        1706404
        1468777
        237627
        S-250609-00565
        0.5
        0.0
        27124
        3324732
        2267789
        1964546
        303243
        0
        0.9
        2.1
        1.5
        327123
        64850
        0
        0.8
        262273
        0.8
        0.3
        1823
        1572
        222671
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        797
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        725
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        860
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        825
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        0
        0.9
        2.1
        1.5
        265396
        39174
        0
        0.9
        226222
        0.8
        0.4
        1145
        976
        178643
        154023
        0.5
        632320
        2338886
        2094844
        244042
        S-250922-01398
        0.2
        0.0
        16397
        1057561
        1304597
        1134843
        169754
        0
        0.9
        2.1
        1.8
        175537
        28685
        0
        0.8
        146852
        0.8
        0.4
        598
        444
        110317
        94811
        0.5
        301773
        1591049
        1376950
        214099
        S-250922-01405
        0.4
        0.0
        28250
        1760848
        1811922
        1648213
        163709
        0
        0.9
        2.1
        1.5
        259546
        38129
        0
        0.9
        221417
        0.8
        0.4
        1103
        943
        184145
        158672
        0.5
        593146
        2256716
        2029245
        227471
        S-250922-01441
        0.4
        0.0
        24955
        2220188
        1871730
        1663972
        207758
        0
        0.9
        2.1
        1.7
        245964
        38166
        0
        0.8
        207798
        0.8
        0.4
        1043
        846
        154800
        133206
        0.5
        604921
        2273537
        2005822
        267715
        S-250922-01448
        0.4
        0.0
        26910
        1855882
        1825042
        1655488
        169554
        0
        0.9
        2.1
        1.6
        253249
        37326
        0
        0.9
        215923
        0.8
        0.4
        1104
        914
        170404
        146804
        0.5
        589907
        2249799
        2019129
        230670
        S-250922-01455
        0.3
        0.0
        19524
        1176089
        1408008
        1253912
        154096
        0
        0.9
        2.1
        1.6
        193777
        29342
        0
        0.8
        164435
        0.8
        0.4
        748
        591
        127251
        110051
        0.5
        355511
        1729784
        1528989
        200795
        S-250922-01485
        0.2
        0.0
        16491
        1313653
        1490512
        1323783
        166729
        0
        0.9
        2.1
        1.6
        186418
        29215
        0
        0.8
        157203
        0.8
        0.5
        730
        520
        103346
        87732
        0.5
        351796
        1781006
        1569238
        211768
        S-250922-01985
        0.4
        0.0
        28162
        2191170
        1928677
        1737696
        190981
        0
        0.9
        2.1
        1.6
        279614
        43961
        0
        0.8
        235653
        0.8
        0.4
        1339
        1122
        198992
        170473
        0.5
        683229
        2408622
        2144944
        263678
        S-250922-01993
        0.2
        0.0
        18298
        1152352
        1415307
        1218874
        196433
        0
        0.9
        2.0
        1.6
        179621
        28214
        0
        0.8
        151407
        0.8
        0.4
        670
        519
        106678
        92389
        0.5
        319293
        1702276
        1463189
        239087
        S-250922-02001
        0.4
        0.0
        26619
        2082533
        1868768
        1685509
        183259
        0
        0.9
        2.1
        1.6
        269168
        41690
        0
        0.8
        227478
        0.8
        0.4
        1222
        1015
        189119
        161976
        0.5
        629609
        2328277
        2075978
        252299
        S-250922-02008
        0.3
        0.0
        26450
        1633098
        1725419
        1559982
        165437
        0
        0.9
        2.1
        1.4
        244789
        36217
        0
        0.9
        208572
        0.8
        0.4
        967
        804
        171317
        147412
        0.5
        537128
        2142492
        1916770
        225722
        S-250922-02015
        0.4
        0.0
        27614
        2426522
        1976888
        1770747
        206141
        0
        0.9
        2.1
        1.5
        274748
        40994
        0
        0.9
        233754
        0.8
        0.4
        1350
        1124
        186793
        162002
        0.5
        690031
        2439779
        2167627
        272152
        S-250922-02022
        0.3
        0.0
        25182
        1608366
        1697089
        1524920
        172169
        0
        0.9
        2.1
        1.5
        230615
        34268
        0
        0.9
        196347
        0.8
        0.4
        901
        759
        151208
        130609
        0.5
        505378
        2079813
        1852635
        227178
        S-250922-02029
        0.3
        0.0
        17145
        1264220
        1394304
        1212923
        181381
        0
        0.9
        2.1
        1.8
        192889
        32433
        0
        0.8
        160456
        0.8
        0.4
        725
        553
        125680
        107328
        0.5
        345677
        1713598
        1481260
        232338
        S-250922-02036
        0.3
        0.0
        25432
        1910593
        1830996
        1652065
        178931
        0
        0.9
        2.1
        1.6
        248744
        36761
        0
        0.9
        211983
        0.8
        0.4
        1062
        890
        161629
        139402
        0.5
        579946
        2242431
        2004340
        238091
        S-250922-02043
        0.4
        0.0
        28276
        2102135
        1945347
        1764001
        181346
        0
        0.9
        2.1
        1.6
        286310
        44234
        0
        0.8
        242076
        0.8
        0.5
        1290
        1085
        204232
        174929
        0.5
        688269
        2437179
        2182091
        255088
        S-251007-02444
        0.4
        0.0
        29510
        2460704
        2050684
        1825255
        225429
        0
        0.9
        2.0
        1.3
        298371
        48043
        0
        0.8
        250328
        0.8
        0.4
        1423
        1210
        214475
        183661
        0.5
        768808
        2564953
        2260454
        304499
        S-251007-02480
        0.3
        0.0
        24952
        1868120
        1780351
        1590966
        189385
        0
        0.9
        2.1
        1.5
        240600
        36147
        0
        0.8
        204453
        0.8
        0.4
        1007
        839
        155107
        133864
        0.5
        552033
        2177065
        1930122
        246943
        S-251007-02559
        0.2
        0.0
        17480
        920717
        1225869
        1059298
        166571
        0
        0.9
        2.0
        1.6
        170413
        28552
        0
        0.8
        141861
        0.8
        0.4
        570
        452
        110636
        95307
        0.5
        270947
        1507488
        1296918
        210570
        Expand table

        Variant Types

        Variants that have been called, looking at variant types. Optionally filtered on label.

        Only passing variants are shown (i.e. non-filtered).

        SNPs are bi-allelic.

        Complex InDels are both an insertion and a deletion.

        Created with MultiQC

        Variant Labels

        Variants that have been called, comparing with known variant sites.

        Only passing variants are shown (i.e. non-filtered).

        Variants contain bi-allelic SNPs, multi-allelic SNPs, simple and complex inserts and deletions.

        Created with MultiQC

        Samtools

        Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Flagstat

        This module parses the output from samtools flagstat

        Created with MultiQC

        Flagstat: Percentage of total

        This module parses the output from samtools flagstat

        Created with MultiQC

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms
        681
        8

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores
        689

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        $ Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content
        546
        143

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content
        689

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution
        689

        All samples have sequences of a single length (151bp)

        Sequence Duplication Levels
        689

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        689 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 4/4 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        302
        12802256
        0.0733%
        CTTATACACATCTCCGAGCCCACGAGACGTAGGCGAGCATCTAGTATGCC
        1
        51249
        0.0003%
        CTTATACACATCTCCGAGCCCACGAGACTCCTACGTCAATCTGGGGGGGG
        1
        50599
        0.0003%
        CTTATACACATCTCCGAGCCCACGAGACCACTAGACCAATCTGGGGGGGG
        1
        47775
        0.0003%

        Adapter Content
        689

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1